FisherTest_GO_BP_MF_CC {seq2pathway} | R Documentation

## A wrapper function to perform the Fisher's exact test, using GO-defined genesets.

### Description

A wrapper function to perform the Fisher's exact test, using GO-defined genesets.

### Usage

    FisherTest_GO_BP_MF_CC(gs, genome=c("hg38","hg19","mm10","mm9"),
                           min_Intersect_Count=5,
                           Ontology=c("GOterm", "BP","MF", "CC","newOntology"),
    			  newOntology=NULL)

### Arguments

`gs` | A characteristic vector of gene symbols, the input gene list.
`genome` | A character specifies the genome type. Currently, choice of "hg38", "hg19", "mm10", and "mm9" is supported.
`min_Intersect_Count` | A number decides the cutoff of the minimum number of intersected genes when reporting Fisher's exact tested results.
`Ontology` | A character specifies the Gene Ontology, choice of "GOterm", "BP","MF", "CC" and "newOntology" is supported.
`newOntology` | A list of two lists with the same ontology IDs. or each ontology ID, the 1st list is the lists of defined genes and the 2nd list is the desceiption.

### Value

A list of 3 data frames, each is a result of Fisher's exact test, using GO CC, BP, MF respectively. Each data frame reports FET results with the following columns.

`GOID` | GO term IDs
`Description` | GO definition and description for the gene-sets
`Fisher_Pvalue` | is the raw P-values
`Fisher_odds` | estimate of the odds ratios
`FDR` | the multi-test adjusted P-values using the Benjamini and Hochberg method
`Intersect_Count` | the sizes of overlap between GO gene members and the input genelist
`GO_gene_inBackground` | the counts of genes among each GO term that are also within the given genome background
`GO_gene_raw_count` | the original counts of genes in each GO term
`Intersect_gene` | the intersecting genes' symbols

### Author(s)

Bin Wang, Xinan Yang

### Examples

      data(dat_chip)
      head(dat_chip)
      data(GO_BP_list,package="seq2pathway.data")
      data(Des_BP_list,package="seq2pathway.data")
      newOntology <- list(GO_BP_list[1:200], Des_BP_list[1:200])
      # A demo run of this funcion
      FS_test<- FisherTest_GO_BP_MF_CC(gs=as.vector(rownames(dat_chip)),
                                     Ontology="newOntology", newOntology=newOntology)
      FS_test

      ## Not run:
      data(dat_chip)
      FS_test<-FisherTest_GO_BP_MF_CC(gs=rownames(dat_chip)[1:20], genome="hg19",
               min_Intersect_Count=1, Ontology="BP")
      FS_test$GO_BP[1:3,]
    ## End(Not run)

[Package seq2pathway version 1.16.0 Index]